mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,031,379 | 0 | G | C | 59.3% | 10.3 / 34.7 | 29 | L14V (CTG→GTG) | yccA | modulator of FtsH protease |
| * | NC_000913 | 2,990,480 | 0 | C | A | 34.7% | 188.7 / 20.5 | 121 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.4% | 199.1 / 20.4 | 131 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 4,540,411 | 0 | C | A | 34.1% | 218.5 / 12.1 | 138 | intergenic (‑910/‑546) | nanC/fimB | N‑acetylneuraminate outer membrane channel/Type 1 fimbriae regulatory protein FimB |
| * | NC_000913 | 2,767,445 | 0 | C | A | 32.0% | 148.5 / 17.0 | 78 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,490,240 | 0 | G | T | 30.7% | 213.3 / 14.9 | 127 | intergenic (‑54/+16) | yfdV/oxc | putative transport protein YfdV/oxalyl‑CoA decarboxylase |
| * | NC_000913 | 847,955 | 0 | G | A | 29.9% | 183.7 / 47.1 | 128 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 58,065 | 0 | C | A | 29.9% | 155.7 / 14.9 | 87 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 2,876,715 | 0 | G | T | 29.2% | 170.2 / 12.1 | 96 | P45P (CCG→CCT) | iap | alkaline phosphatase isozyme conversion protein |
| * | NC_000913 | 2,288,418 | 0 | G | T | 29.0% | 246.4 / 16.2 | 139 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 3,054,894 | 0 | G | T | 28.7% | 122.5 / 14.2 | 80 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,054,886 | 0 | G | T | 28.7% | 147.9 / 21.0 | 87 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,157,420 | 0 | C | A | 28.0% | 194.9 / 10.9 | 100 | L266L (CTC→CTA) | dkgA | methylglyoxal reductase DkgA |
| * | NC_000913 | 2,466,633 | 0 | C | A | 26.7% | 230.5 / 11.0 | 116 | P30H (CCT→CAT) | intS | prophage CPS‑53 integrase |
| * | NC_000913 | 1,697,301 | 0 | G | T | 25.9% | 223.5 / 10.2 | 108 | S247Y (TCC→TAC) | hdhA | 7‑alpha‑hydroxysteroid dehydrogenase |
| * | NC_000913 | 1,902,613 | 0 | C | A | 25.6% | 177.7 / 10.6 | 86 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 1,502,772 | 0 | G | A | 25.4% | 180.3 / 28.9 | 112 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 1,922,815 | 0 | C | A | 25.2% | 214.3 / 18.3 | 111 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 1,286,870 | 0 | C | A | 25.0% | 124.6 / 22.6 | 61 | S54S (TCC→TCA) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 3,789,274 | 0 | C | A | 24.2% | 247.4 / 10.8 | 120 | E270* (GAG→TAG) | waaH | UDP‑glucuronate:LPS(HepIII) glycosyltransferase |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 780629 | 85 (0.960) | 11 (0.170) | 11/436 | 3.5 | 13.8% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 74 (1.130) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 2518116 | 65 (0.730) | 7 (0.110) | 7/426 | 4.7 | 13.2% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 45 (0.700) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 3648146 | 106 (1.200) | 7 (0.100) | 7/472 | 5.1 | 7.1% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 98 (1.380) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 781369 = | 57 (0.640) | 14 (0.160) +G |
10/586 | 5.1 | 18.4% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521127 | 68 (0.770) | intergenic (+1/‑46) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | 781369 = | 57 (0.640) | 14 (0.160) +GG |
10/584 | 5.1 | 16.8% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 83 (0.940) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 1286906 | 53 (0.600) | 8 (0.100) | 8/548 | 5.5 | 14.6% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 44 (0.530) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1287084 | 47 (0.530) | 7 (0.080) | 7/548 | 5.8 | 13.8% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 44 (0.530) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1166125 | 88 (0.990) | 8 (0.100) | 7/558 | 5.9 | 9.4% | coding (41/1305 nt) | ndh | NADH:quinone oxidoreductase II |
| ? | NC_000913 | 1166621 = | 71 (0.850) | coding (537/1305 nt) | ndh | NADH:quinone oxidoreductase II | |||||
| * | ? | NC_000913 | = 2817942 | 69 (0.780) | 6 (0.070) | 6/548 | 6.2 | 9.2% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 54 (0.650) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 1287262 | 56 (0.630) | 5 (0.060) | 5/546 | 6.7 | 9.7% | noncoding (67/85 nt) | tyrV | tRNA‑Tyr |
| ? | NC_000913 | 1287382 = | 41 (0.500) | intergenic (‑54/+156) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr | |||||